Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/change_sp.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl -w
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $infile = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $changefile = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 my $outfile = $ARGV[2];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 open(IN, "$infile") or exit;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 open(CHANGE, "$changefile");
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 open(OUT, ">$outfile") or exit;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my %speciesFor; #Hash to associate code with species name
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 while (<CHANGE>)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 chomp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 my $currentinput = "$_";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 if($currentinput =~m /\t/){ #must have a tab otherwise wrong file format
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 if($currentinput =~m /\t\t/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 print OUT "ERROR: file contains 2 tabs in a row. Check phytab format.\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 die("ERROR: file contains 2 tabs in a row. Check it is in phytab format");
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 my @changepair = split(/\t/, $currentinput);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 my $codename=$changepair[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 my $sp_name = $changepair[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 if (exists $speciesFor{$codename}) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 print OUT "ERROR: Species name specification for $codename is duplicated\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 die("ERROR: Species name specifiation for for $codename is duplicated\n");
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 $speciesFor{$codename}=$sp_name;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 die "ERROR: Species conversion table must be genefamily\tmodel and contain no blank lines\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 while (<IN>) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 chomp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 my $currentinput = "$_";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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41 if($currentinput =~m /\t/){ #must have a tab otherwise wrong file format
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 if($currentinput =~m /\t\t/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 print OUT "ERROR: file contains 2 tabs in a row. Check phytab format.\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 die;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 my @changepair = split(/\t/, $currentinput);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 my $sp_name=$changepair[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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49 if (exists $speciesFor{$sp_name}) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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50 $currentinput =~s /$sp_name/$speciesFor{$sp_name}/ ;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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51 print OUT $currentinput."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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52 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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53 print OUT $currentinput."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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54 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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55 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 die "ERROR: Input a PHYTAB file in Tabular format\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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58 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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59 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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60 close(IN);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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61 close(OUT);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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62 close(CHANGE);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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63
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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64 sub change
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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65 {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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66
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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67 my $changetext = shift;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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68 $changetext =~ s/ /_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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69 return $changetext;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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70 }